A modern pipeline for academic collaboration

Rationale

As scientists, we spend a lot of time coding and writing.

Unfortunately, both activities involve repetitive behaviors and suboptimal routines…

For example, we might…

  • Duplicate our manuscript many times during co-edition
  • Struggle with references and bibliographies
  • Spend hours (days) reformating papers for resubmissions
  • Paste many variants of a figure in our presentation/report
  • Spend way to much title aligning items on Powerpoint
  • Feel like it is a big effort to put together a few slides or a report to describe our results
  • Have no idea of how we could participate or animate large-scale collaborations ! 🤪

Time wasted reduces your happiness

And this is particularly true when it comes with collaborating with our peers.

What prevents us from collaborating more smoothly?

  • Endless multiplication of communication channels (Mattermost 😇)

  • Data and code on local computers

  • Suboptimal coding practices (no virtual envs, no version control, absolute paths)

  • Lack of knowledge regarding others interests, skills and activities

  • Dependence upon Google Docs is increasingly problematic

    • And Google Docs is not even great
  • Unnecessary differences in software use.

  • …?

A (tiny) reason to hope!

Most Cophy-makers already use Zotero or are willing to change. Users of Latex will be fine anyways.

A (bigger) reason to worry?

It seems that Cophy-makers use a huge diversity of IDE, and that we are still a minority to use Git-based version control.

PyCharm-Matlab people: who are you, what are your networks?🕵️

Towards a straightforward solution

Correlation does not imply causation, but those who are still not using Git may still need to install Visual Studio Code.